(v3.0.1.9018) fixes #249

updates AB groups

R/aa_globals.R

@@ -34,37 +34,37 @@ EUCAST_VERSION_BREAKPOINTS <- list(
     version_txt = "v15.0",
     year = 2025,
     title = "'EUCAST Clinical Breakpoint Tables'",
-    url = "https://www.eucast.org/clinical_breakpoints/"
+    url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
   ),
   "14.0" = list(
     version_txt = "v14.0",
     year = 2024,
     title = "'EUCAST Clinical Breakpoint Tables'",
-    url = "https://www.eucast.org/clinical_breakpoints/"
+    url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
   ),
   "13.1" = list(
     version_txt = "v13.1",
     year = 2023,
     title = "'EUCAST Clinical Breakpoint Tables'",
-    url = "https://www.eucast.org/clinical_breakpoints/"
+    url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
   ),
   "12.0" = list(
     version_txt = "v12.0",
     year = 2022,
     title = "'EUCAST Clinical Breakpoint Tables'",
-    url = "https://www.eucast.org/clinical_breakpoints/"
+    url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
   ),
   "11.0" = list(
     version_txt = "v11.0",
     year = 2021,
     title = "'EUCAST Clinical Breakpoint Tables'",
-    url = "https://www.eucast.org/clinical_breakpoints/"
+    url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
   ),
   "10.0" = list(
     version_txt = "v10.0",
     year = 2020,
     title = "'EUCAST Clinical Breakpoint Tables'",
-    url = "https://www.eucast.org/ast_of_bacteria/previous_versions_of_documents/"
+    url = "https://www.eucast.org/bacteria/document-archive/"
   )
 )
 EUCAST_VERSION_EXPERT_RULES <- list(
@@ -72,19 +72,19 @@ EUCAST_VERSION_EXPERT_RULES <- list(
     version_txt = "v3.3",
     year = 2021,
     title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
-    url = "https://www.eucast.org/expert_rules_and_expected_phenotypes"
+    url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/"
   ),
   "3.2" = list(
     version_txt = "v3.2",
     year = 2020,
     title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
-    url = "https://www.eucast.org/expert_rules_and_expected_phenotypes"
+    url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/"
   ),
   "3.1" = list(
     version_txt = "v3.1",
     year = 2016,
     title = "'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes'",
-    url = "https://www.eucast.org/expert_rules_and_expected_phenotypes"
+    url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/"
   )
 )
 EUCAST_VERSION_EXPECTED_PHENOTYPES <- list(
@@ -92,7 +92,7 @@ EUCAST_VERSION_EXPECTED_PHENOTYPES <- list(
     version_txt = "v1.2",
     year = 2023,
     title = "'EUCAST Expected Resistant Phenotypes'",
-    url = "https://www.eucast.org/expert_rules_and_expected_phenotypes"
+    url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/"
   )
 )
 

R/aa_helper_functions.R

@@ -1042,24 +1042,8 @@ get_current_column <- function() {
 
   # cur_column() doesn't always work (only allowed for certain conditions set by dplyr), but it's probably still possible:
   frms <- lapply(sys.frames(), function(env) {
-    if (tryCatch(!is.null(env$i), error = function(e) FALSE)) {
-      if (!is.null(env$tibble_vars)) {
-        # for mutate_if()
-        # TODO remove later, was part of older dplyr versions (at least not in dplyr 1.1.4)
-        env$tibble_vars[env$i]
-      } else {
-        # for mutate(across())
-        if (!is.null(env$data) && is.data.frame(env$data)) {
-          df <- env$data
-        } else {
-          df <- tryCatch(get_current_data(NA, 0), error = function(e) NULL)
-        }
-        if (is.data.frame(df)) {
-          colnames(df)[env$i]
-        } else {
-          env$i
-        }
-      }
+    if (all(c("dots", "i") %in% names(env))) {
+      names(env$dots)[env$i]
     } else {
       NULL
     }

R/ab.R

@@ -54,7 +54,7 @@
 #' @section Source:
 #' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/}
 #'
-#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
+#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm}
 #' @aliases ab
 #' @return A [character] [vector] with additional class [`ab`]
 #' @seealso

R/av.R

@@ -51,7 +51,7 @@
 #' @section Source:
 #' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/}
 #'
-#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
+#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm}
 #' @aliases av
 #' @return A [character] [vector] with additional class [`ab`]
 #' @seealso

R/disk.R

@@ -121,7 +121,7 @@ as.disk <- function(x, na.rm = FALSE) {
       cur_col <- get_current_column()
       warning_("in `as.disk()`: ", na_after - na_before, " result",
         ifelse(na_after - na_before > 1, "s", ""),
-        ifelse(is.null(cur_col), "", paste0(" in index '", cur_col, "'")),
+        ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
         " truncated (",
         round(((na_after - na_before) / length(x)) * 100),
         "%) that were invalid disk zones: ",

R/mic.R

@@ -260,7 +260,7 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all") {
     cur_col <- get_current_column()
     warning_("in `as.mic()`: ", na_after - na_before, " result",
       ifelse(na_after - na_before > 1, "s", ""),
-      ifelse(is.null(cur_col), "", paste0(" in index '", cur_col, "'")),
+      ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
       " truncated (",
       round(((na_after - na_before) / length(x)) * 100),
       "%) that were invalid MICs: ",

R/sir.R

@@ -165,7 +165,7 @@
 #'
 #' The function [is_sir_eligible()] returns `TRUE` when a column contains at most 5% potentially invalid antimicrobial interpretations, and `FALSE` otherwise. The threshold of 5% can be set with the `threshold` argument. If the input is a [data.frame], it iterates over all columns and returns a [logical] vector.
 #' @section Interpretation of SIR:
-#' In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (<https://www.eucast.org/newsiandr>).
+#' In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (<https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/>).
 #'
 #' This AMR package follows insight; use [susceptibility()] (equal to [proportion_SI()]) to determine antimicrobial susceptibility and [count_susceptible()] (equal to [count_SI()]) to count susceptible isolates.
 #' @return Ordered [factor] with new class `sir`
@@ -179,7 +179,7 @@
 #' - **CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type != "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type != "animal")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). <https://clsi.org/standards/products/microbiology/documents/m100/>.
 #' - **CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). <https://clsi.org/standards/products/veterinary-medicine/documents/vet01/>.
 ###### TODO  - **CLSI VET09: Understanding Susceptibility Test Data as a Component of Antimicrobial Stewardship in Veterinary Settings**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). <https://clsi.org/standards/products/veterinary-medicine/documents/vet09/>.
-#' - **EUCAST Breakpoint tables for interpretation of MICs and zone diameters**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`, *European Committee on Antimicrobial Susceptibility Testing* (EUCAST). <https://www.eucast.org/clinical_breakpoints>.
+#' - **EUCAST Breakpoint tables for interpretation of MICs and zone diameters**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`, *European Committee on Antimicrobial Susceptibility Testing* (EUCAST). <https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/>.
 #' - **WHONET** as a source for machine-reading the clinical breakpoints ([read more here](https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet)), 1989-`r max(as.integer(gsub("[^0-9]", "", AMR::clinical_breakpoints$guideline)))`, *WHO Collaborating Centre for Surveillance of Antimicrobial Resistance*. <https://whonet.org/>.
 #'
 #' @inheritSection AMR Download Our Reference Data
@@ -593,7 +593,7 @@ as.sir.default <- function(x,
         cur_col <- get_current_column()
         warning_("in `as.sir()`: ", na_after - na_before, " result",
           ifelse(na_after - na_before > 1, "s", ""),
-          ifelse(is.null(cur_col), "", paste0(" in index '", cur_col, "'")),
+          ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
           " truncated (",
           round(((na_after - na_before) / length(x)) * 100),
           "%) that were invalid antimicrobial interpretations: ",